private void calculateArrowsForward(Node x, Node y, Graph graph) {
clearArrow(x, y);
if (!knowledgeEmpty()) {
if (getKnowledge().isForbidden(x.getName(), y.getName())) {
return;
}
}
List<Node> naYX = getNaYX(x, y, graph);
List<Node> t = getTNeighbors(x, y, graph);
DepthChoiceGenerator gen = new DepthChoiceGenerator(t.size(), t.size());
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> s = GraphUtils.asList(choice, t);
if (!knowledgeEmpty()) {
if (!validSetByKnowledge(y, s)) {
continue;
}
}
double bump = insertEval(x, y, s, naYX, graph);
if (bump > 0.0) {
Arrow arrow = new Arrow(bump, x, y, s, naYX);
sortedArrows.add(arrow);
addLookupArrow(x, y, arrow);
}
}
}
/** Returns true iif the given set forms a clique in the given graph. */
private static boolean isClique(List<Node> nodes, Graph graph) {
for (int i = 0; i < nodes.size() - 1; i++) {
for (int j = i + 1; j < nodes.size(); j++) {
if (!graph.isAdjacentTo(nodes.get(i), nodes.get(j))) {
return false;
}
}
}
return true;
}
private static double characteristicPathLength(Graph g) {
List<Node> nodes = g.getNodes();
int total = 0;
int count = 0;
for (int i = 0; i < nodes.size(); i++) {
for (int j = i; j < nodes.size(); j++) {
int shortest = shortestPath(nodes.get(i), nodes.get(j), g);
total += shortest;
count++;
}
}
return total / (double) count;
}
private String clusterSizes(List<List<Node>> partition, List<List<Node>> trueClusters) {
String s = "";
FOR:
for (int i = 0; i < partition.size(); i++) {
List<Node> cluster = partition.get(i);
s += cluster.size();
for (List<Node> trueCluster : trueClusters) {
if (trueCluster.containsAll(cluster)) {
// Collections.sort(trueCluster);
// Collections.sort(cluster);
// System.out.println(trueCluster + " " + cluster);
s += "p";
if (i < partition.size() - 1) {
s += ",";
}
continue FOR;
}
}
if (i < partition.size() - 1) {
s += ",";
}
}
return s;
}
private int numClustered(List<List<Node>> partition) {
int sum = 0;
for (int i = 0; i < partition.size(); i++) {
List<Node> cluster = partition.get(i);
sum += cluster.size();
}
return sum;
}
/** Tests to see if d separation facts are symmetric. */
public void testDSeparation2() {
EdgeListGraphSingleConnections graph =
new EdgeListGraphSingleConnections(
new Dag(GraphUtils.randomGraph(7, 0, 14, 30, 15, 15, true)));
List<Node> nodes = graph.getNodes();
int depth = -1;
for (int i = 0; i < nodes.size(); i++) {
for (int j = i; j < nodes.size(); j++) {
Node x = nodes.get(i);
Node y = nodes.get(j);
List<Node> theRest = new ArrayList<Node>(nodes);
// theRest.remove(x);
// theRest.remove(y);
DepthChoiceGenerator gen = new DepthChoiceGenerator(theRest.size(), depth);
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> z = new LinkedList<Node>();
for (int k = 0; k < choice.length; k++) {
z.add(theRest.get(choice[k]));
}
boolean dConnectedTo = graph.isDConnectedTo(x, y, z);
boolean dConnectedTo1 = graph.isDConnectedTo(y, x, z);
if (dConnectedTo != dConnectedTo1) {
System.out.println(x + " d connected to " + y + " given " + z);
System.out.println(graph);
System.out.println("dconnectedto = " + dConnectedTo);
System.out.println("dconnecteto1 = " + dConnectedTo1);
fail();
}
}
}
}
}
// Invalid if then nodes or graph changes.
private void calculateArrowsBackward(Node x, Node y, Graph graph) {
if (x == y) {
return;
}
if (!graph.isAdjacentTo(x, y)) {
return;
}
if (!knowledgeEmpty()) {
if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
return;
}
}
List<Node> naYX = getNaYX(x, y, graph);
clearArrow(x, y);
List<Node> _naYX = new ArrayList<Node>(naYX);
DepthChoiceGenerator gen = new DepthChoiceGenerator(_naYX.size(), _naYX.size());
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> H = GraphUtils.asList(choice, _naYX);
if (!knowledgeEmpty()) {
if (!validSetByKnowledge(y, H)) {
continue;
}
}
double bump = deleteEval(x, y, H, naYX, graph);
if (bump > 0.0) {
Arrow arrow = new Arrow(bump, x, y, H, naYX);
sortedArrows.add(arrow);
addLookupArrow(x, y, arrow);
}
}
}
/** Tests to see if d separation facts are symmetric. */
public void testDSeparation() {
EdgeListGraphSingleConnections graph =
new EdgeListGraphSingleConnections(
new Dag(GraphUtils.randomGraph(7, 0, 7, 30, 15, 15, true)));
System.out.println(graph);
List<Node> nodes = graph.getNodes();
int depth = -1;
for (int i = 0; i < nodes.size(); i++) {
for (int j = i + 1; j < nodes.size(); j++) {
Node x = nodes.get(i);
Node y = nodes.get(j);
List<Node> theRest = new ArrayList<Node>(nodes);
theRest.remove(x);
theRest.remove(y);
DepthChoiceGenerator gen = new DepthChoiceGenerator(theRest.size(), depth);
int[] choice;
while ((choice = gen.next()) != null) {
List<Node> z = new LinkedList<Node>();
for (int k = 0; k < choice.length; k++) {
z.add(theRest.get(choice[k]));
}
if (graph.isDSeparatedFrom(x, y, z) != graph.isDSeparatedFrom(y, x, z)) {
fail(
SearchLogUtils.independenceFact(x, y, z)
+ " should have same d-sep result as "
+ SearchLogUtils.independenceFact(y, x, z));
}
}
}
}
}
private static int weightedRandom(List<Node> nodes, Graph graph) {
int total = 0;
int n = nodes.size();
for (int b = 0; b < n; b++) {
total = weight(nodes, graph, total, b);
}
int r = RandomUtil.getInstance().nextInt(total);
int count = 0;
int index = 0;
for (int b = 0; b < n; b++) {
count = weight(nodes, graph, count, b);
if (r <= count) {
index = b;
break;
}
}
return index;
}